The objectives of the proposed research project are the continued design, development, and evaluation of Fourier ion cyclotron resonance (FT-ICR) based techniques for the analysis and characterization of thermally labile biomolecules. During the past three to five years, major progress has been make in the development of high mass FT-ICR. However, certain aspects of the experimental results reveal specific problems which we attribute to trapping and/or detection of large (> m/z 2500-3000) ionic systems using FT-ICR. Probing and understanding these problems is further complicated by the fact that existing FT_ICR systems are not capable of making absolute measurements. That is, the signals measured give relative abundance of the ions trapped in the ion cell, but it is difficult to relate relative abundance measurements to absolute numbers of ions. Recent work has shown that ion detection is strongly dependent upon the initial ion motion, thus ion detection strongly discriminates against ions which possess non-thermal kinetic energies and which are initially out-of-phase with respect to the rf excitation. Absolute measurements are important because sensitivity and mass resolution are directly dependent upon the numbers of ions trapped in the ion cell. As a first approach to addressing issues related to trapping and detection efficiency of FT-ICR we have constructed a prototype time-of- flight/FT-ICR apparatus. This instrument will be used to investigate various aspects of trapping and detection of high mass (m/z 2500-15000) organic ions. An integral part of this instrument is the interface between the time-of-flight and FT-ICR instruments, e.g., the two-dimensional quadrupole lens assembly. This lensing element is potentially useful in may areas of FT-ICR, and especially on instruments utilizing external ion sources. In the later stages of the program, the two-dimensional lens assembly will be used to evaluate the use of different ion sources and structural probe methods for analyzing and characterizing large peptides and related systems.